Is it possible to isolate parts of an armature so the mesh will never deform?
You could select the shell in Edit mode, go in the Properties panel > Data > Vertex Groups, on the right of the vertex groups list, click on the down arrow button and choose Remove From All Groups. You could now assign these vertices to your big body bone vertex group, or create a new bone, child of this big bone, give it a name, create a vertex group with the same name and assign your shell to it, so that you have a bone completely dedicated to the shell, if you ever need it to move slightly differently sometimes.

You say "I thought that I could paint the weights by bone, but it looks like it's only possible to do so by the whole armature (at least from what I can tell)", I'm not sure what you're saying, maybe you're missing that if you switch your armature to Pose mode, then select your mesh and switch to Weight Paint mode, you can select one bone and see what influence (i.e. vertices groups) it has on the mesh.